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- PDB-9hrw: The RSL - pctx complex, P63 form -

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Basic information

Entry
Database: PDB / ID: 9hrw
TitleThe RSL - pctx complex, P63 form
ComponentsFucose-binding lectin protein
KeywordsSUGAR BINDING PROTEIN / Complex
Function / homologyFucose-specific lectin / Fungal fucose-specific lectin / carbohydrate binding / metal ion binding / : / beta-D-fructopyranose / Fucose-binding lectin protein
Function and homology information
Biological speciesRalstonia solanacearum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.07 Å
AuthorsWren, C.P. / Flood, R.J. / Crowley, P.B.
Funding support Ireland, 1items
OrganizationGrant numberCountry
Science Foundation Ireland12/RC/2275_P2 Ireland
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: Protein Recognition and Assembly by a Phosphocavitand.
Authors: Wren, C.P. / Flood, R.J. / Mockler, N.M. / Savko, M. / Malinska, M. / Shi, Q. / Crowley, P.B.
History
DepositionDec 18, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fucose-binding lectin protein
B: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,80412
Polymers19,4672
Non-polymers3,33710
Water4,648258
1
A: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4387
Polymers9,7341
Non-polymers1,7046
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3675
Polymers9,7341
Non-polymers1,6334
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.078, 46.078, 139.565
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2
Components on special symmetry positions
IDModelComponents
11A-289-

HOH

21A-291-

HOH

31A-313-

HOH

41A-337-

HOH

51B-308-

HOH

61B-315-

HOH

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Components

#1: Protein Fucose-binding lectin protein / Putative fucose-binding lectin protein


Mass: 9733.562 Da / Num. of mol.: 2 / Mutation: 0
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia solanacearum (bacteria)
Gene: E7Z57_08365, RSP795_21825, RSP822_19650, RUN39_v1_50103
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0S4TLR1
#2: Sugar
ChemComp-BDF / beta-D-fructopyranose / beta-D-fructose / D-fructose / fructose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DFrupbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-fructopyranoseCOMMON NAMEGMML 1.0
b-D-FrupIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FruSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-A1IXG / phosphated-cyclotrixylohydroquinoylene


Mass: 636.417 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H27O12P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 18% PEG 6000, 1 M lithium chloride, 0.1 M tri-Sodium citrate pH 4.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 11, 2023
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.07→69.78 Å / Num. obs: 71473 / % possible obs: 97.8 % / Redundancy: 16 % / Biso Wilson estimate: 10.17 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.025 / Rrim(I) all: 0.111 / Net I/σ(I): 10.6
Reflection shellResolution: 1.07→1.09 Å / Redundancy: 2.5 % / Rmerge(I) obs: 1.176 / Num. unique obs: 2731 / CC1/2: 0.334 / Rpim(I) all: 0.863 / Rrim(I) all: 1.471 / % possible all: 75.9

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
autoPROCdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.07→69.78 Å / SU ML: 0.1335 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.7426
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1837 3504 4.91 %
Rwork0.1687 67900 -
obs0.1694 71404 97.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.92 Å2
Refinement stepCycle: LAST / Resolution: 1.07→69.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1376 0 218 258 1852
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091665
X-RAY DIFFRACTIONf_angle_d1.33792357
X-RAY DIFFRACTIONf_chiral_restr0.0928229
X-RAY DIFFRACTIONf_plane_restr0.0077388
X-RAY DIFFRACTIONf_dihedral_angle_d10.8847627
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.07-1.090.3311860.35592019X-RAY DIFFRACTION73.65
1.09-1.10.34141520.32252286X-RAY DIFFRACTION83.61
1.1-1.120.27941380.30242527X-RAY DIFFRACTION90.96
1.12-1.140.27161610.25752629X-RAY DIFFRACTION95.84
1.14-1.160.26931280.2362791X-RAY DIFFRACTION99.18
1.16-1.180.2361150.21652777X-RAY DIFFRACTION99.97
1.18-1.20.21251440.19672749X-RAY DIFFRACTION99.97
1.2-1.220.21751500.19572805X-RAY DIFFRACTION100
1.22-1.240.22191220.18712808X-RAY DIFFRACTION100
1.24-1.270.19381420.18062742X-RAY DIFFRACTION100
1.27-1.30.21571780.17222761X-RAY DIFFRACTION99.97
1.3-1.330.20151360.17292769X-RAY DIFFRACTION100
1.33-1.370.21081360.16972789X-RAY DIFFRACTION99.97
1.37-1.410.17271480.16382775X-RAY DIFFRACTION100
1.41-1.460.15471370.15752791X-RAY DIFFRACTION100
1.46-1.510.17681140.162822X-RAY DIFFRACTION100
1.51-1.570.18281540.15342748X-RAY DIFFRACTION99.97
1.57-1.640.1751510.15252788X-RAY DIFFRACTION100
1.64-1.730.16831500.15332762X-RAY DIFFRACTION100
1.73-1.830.18271530.1622772X-RAY DIFFRACTION100
1.83-1.980.1711270.15722799X-RAY DIFFRACTION99.97
1.98-2.170.16671510.15762790X-RAY DIFFRACTION100
2.17-2.490.18361540.16562772X-RAY DIFFRACTION100
2.49-3.130.18291450.16862798X-RAY DIFFRACTION99.97
3.14-69.780.1421320.13992831X-RAY DIFFRACTION99.87

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